Search Results - "Ayton, Gary"

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models by Noid, W G, Chu, Jhih-Wei, Ayton, Gary S, Krishna, Vinod, Izvekov, Sergei, Voth, Gregory A, Das, Avisek, Andersen, Hans C

“…Coarse-grained (CG) models provide a computationally efficient method for rapidly investigating the long time- and length-scale processes that play a critical…”
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Multiscale modeling of biomolecular systems: in serial and in parallel by Ayton, Gary S, Noid, Will G, Voth, Gregory A

“…Considerable progress has been recently achieved in the multiscale modeling of complex biological processes. Multiscale models have now investigated the…”
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The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models by Noid, W G, Liu, Pu, Wang, Yanting, Chu, Jhih-Wei, Ayton, Gary S, Izvekov, Sergei, Andersen, Hans C, Voth, Gregory A

“…The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a…”
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Multiscale Computer Simulation of the Immature HIV-1 Virion by Ayton, Gary S., Voth, Gregory A.

“…Multiscale computer simulations, employing a combination of experimental data and coarse-graining methods, are used to explore the structure of the immature…”
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Systematic multiscale simulation of membrane protein systems by Ayton, Gary S, Voth, Gregory A

“…Current multiscale simulation approaches for membrane protein systems vary depending on their degree of connection to the underlying molecular scale…”
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Multiscale Coarse-Graining and Structural Correlations:  Connections to Liquid-State Theory by Noid, W. G, Chu, Jhih-Wei, Ayton, Gary S, Voth, Gregory A

“…A statistical mechanical framework elucidates the significance of structural correlations between coarse-grained (CG) sites in the multiscale coarse-graining…”
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Hybrid Coarse-Graining Approach for Lipid Bilayers at Large Length and Time Scales by Ayton, Gary S, Voth, Gregory A

“…A hybrid analytic−systematic (HAS) coarse-grained (CG) lipid model is developed and employed in a large-scale simulation of a liposome. The methodology is…”
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Membrane Binding by the Endophilin N-BAR Domain by Cui, Haosheng, Ayton, Gary S., Voth, Gregory A.

“…The structure of the endophilin N-terminal amphipathic helix Bin/Amphiphysin/Rvs-homology (N-BAR) domain is unique because of an additional insert helix under…”
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Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales by Ayton, Gary S, Lyman, Edward, Voth, Gregory A

“…An overall multiscale simulation strategy for large scale coarse-grain simulations of membrane protein systems is presented. The protein is modeled as a…”
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New Insights into BAR Domain-Induced Membrane Remodeling by Ayton, Gary S., Lyman, Edward, Krishna, Vinod, Swenson, Richard D., Mim, Carsten, Unger, Vinzenz M., Voth, Gregory A.

“…Mesoscopic simulations and electron microscopy of N-BAR domain-induced liposome remodeling are used to characterize the process of liposome tubulation and…”
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Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-Grained Analysis by Krishna, Vinod, Ayton, Gary S., Voth, Gregory A.

“…Coarse-grained models of the HIV-1 CA dimer are constructed based on all-atom molecular dynamics simulations. Coarse-grained representations of the capsid…”
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Multiscale simulation of protein mediated membrane remodeling by Ayton, Gary S., Voth, Gregory A.

“…Proteins interacting with membranes can result in substantial membrane deformations and curvatures. This effect is known in its broadest terms as membrane…”
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Multiscale simulation of transmembrane proteins by Ayton, Gary S., Voth, Gregory A.

“…Multiscale simulation is employed to examine changes in atomistic-level protein structure due to long wavelength membrane undulations and plane stress fields…”
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Impact of Early Intervention on Outcome After Mild Traumatic Brain Injury in Children by Ponsford, Jennie, Willmott, Catherine, Rothwell, Andrew, Cameron, Peter, Ayton, Gary, Nelms, Robyn, Curran, Carolyn, Ng, Kim

“…The impact of mild head injury or mild traumatic brain injury (TBI) in children is variable, and determinants of outcome remain poorly understood. There have…”
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Extending the fluctuation theorem to describe reaction coordinates by Paramore, Sterling, Ayton, Gary S, Voth, Gregory A

“…The fluctuation theorem describes the distribution of work done on small systems which have been pushed out of equilibrium in response to an external field…”
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Coupling Field Theory with Continuum Mechanics: A Simulation of Domain Formation in Giant Unilamellar Vesicles by Ayton, Gary S., McWhirter, J. Liam, McMurtry, Patrick, Voth, Gregory A.

“…Domain formation is modeled on the surface of giant unilamellar vesicles using a Landau field theory model for phase coexistence coupled to elastic deformation…”
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Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations by Chang, Rakwoo, Ayton, Gary S, Voth, Gregory A

“…A multiscale method is presented to bridge between the atomistic and mesoscopic membrane systems. The atomistic model in this case is the united atom…”
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A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics by Ayton, Gary S, McWhirter, J Liam, Voth, Gregory A

“…A new mesoscopic membrane model is developed in order to examine long-wavelength structural and dynamical membrane phenomena. Two different explicit mesoscopic…”
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Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation by Ayton, Gary S., Blood, Philip D., Voth, Gregory A.

“…Liposome remodeling processes (e.g., vesiculation and tubulation) due to N-BAR domain interactions with the lipid bilayer are explored with a multi-scale…”
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Mesoscopic Lateral Diffusion in Lipid Bilayers by Ayton, Gary S., Voth, Gregory A.

“…The lateral diffusion in bilayers is modeled with a multiscale mesoscopic simulation. The methodology consists of two simulations, where the first employs…”
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